Consider adding checkM to the pipeline

[jfy133]

Description of feature

CheckM is been updated to allow 'custom' paths to internal databases. We could now try adding it to the pipeline (Again)

[maxibor]

Checkm2 is (kind of) out (preprint, repo), and from a brief look at the code, it looks that they reproduced the same mistake with singularity.
But it's been caught early enough (chklovski/CheckM2#15), so hopefully by the time they release, it should work fine with singularity

So I would suggest waiting for the fix and the release, and then integrate directly checkm2 instead.

[jfy133]

Done!